Joseph Whitaker Thompson (August 19, 1861, Stroudsburg, Pennsylvania – January 7, 1946) was a United States federal judge.
Thompson graduated from the University of Pennsylvania Law School with an LL.B. in 1887. He was an Assistant United States Attorney for the Eastern District of Pennsylvania from 1900–1904, and then the United States Attorney for that district until 1912.
Thompson was nominated to the United States District Court for the Eastern District of Pennsylvania by President William Howard Taft on June 5, 1912, to a seat vacated by John B. McPherson. He was confirmed by the United States Senate on June 16, 1912, and received his commission on July 16, 1912. Service terminated on February 3, 1931, due to appointment to the United States Court of Appeals for the Third Circuit. He was appointed to that court by President Herbert Hoover on December 4, 1930, to a new seat created by 46 Stat. 538. He was confirmed by the Senate on January 22, 1931, and received his commission on January 29, 1931. He assumed senior status on May 1, 1938, and served in that capacity until his death.